Published April 29, 2020
| Version v1
Journal article
Open
pyGenomeTracks main figure data
Creators
- 1. EPFL SV ISREC UPDUB, Lausanne, Switzerland
- 2. Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- 3. Albert-Ludwigs-Universität Freiburg, Germany
Description
Data used for pyGenomeTracks publication, D. melanogaster dm3; cell type Kc167.
chromatinStates_kc.bed: Van Bortle et al. 2014
CP190.bw: Wood et al. 2011
dm3_genes_compact_no_cg.bed: Ensembl version 78
H3K36me3.bw: The modENCODE Consortium 2010
HiC_Cubenas.h5: Cubeñas-Potts et al. 2016
HiC_Li_et_al.h5: Li et al. 2015
RNAPII.bw: Li et al. 2015
HiC_Cubenas.h5 and HiC_Li_et_al.h5 were created with HiCExplorers hicBuildMatrix, the TAD-files were computed on HiC_Cubenas.h5 with HiCExplorers hicFindTADs. The dm3 genes were pruned by us for a better visual presentation. The file test.arcs was artificially created by us.
The most files were downloaded from http://chorogenome.ie-freiburg.mpg.de/data_sources.html
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Additional details
References
- Cubeñas-Potts, C. et al., 2016. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic acids research.
- Li, L.et al. 2015. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing
- Wood, Ashley M., et al. "Regulation of chromatin organization and inducible gene expression by a Drosophila insulator." Molecular cell 44.1 (2011): 29-38.
- Van Bortle, Kevin, et al. "Insulator function and topological domain border strength scale with architectural protein occupancy." Genome biology 15.5 (2014): R82.